tripper 0.4.2__tar.gz → 0.4.3__tar.gz

{tripper-0.4.2 → tripper-0.4.3}/.github/workflows/ci_cd_updated_main.yml

@@ -24,7 +24,7 @@ jobs:
       update_python_api_ref: true
       package_dirs: tripper
       update_docs_landing_page: true
-      python_version: "3.9"
+      python_version: "3.12"
       doc_extras: "[docs]"
       changelog_exclude_labels: "skip_changelog,duplicate,question,invalid,wontfix"
       docs_framework: mkdocs

{tripper-0.4.2 → tripper-0.4.3}/.github/workflows/ci_tests.yml

@@ -79,7 +79,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13", "3.14.0-rc.2"]
 
     steps:
     - name: Checkout tripper
@@ -118,7 +118,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12", "3.13", "3.14.0-rc.2"]
 
     steps:
     - name: Checkout tripper

{tripper-0.4.2 → tripper-0.4.3}/.hooks/generate-context-and-doc.sh

@@ -10,5 +10,11 @@ python tripper/datadoc/keywords.py \
     --keywords=docs/datadoc/keywords.md \
     --prefixes=docs/datadoc/prefixes.md
 
+python tripper/datadoc/keywords.py \
+    --context=tripper/context/process/0.1/context.json \
+    --keywords=docs/datadoc/keywords-process.md \
+    --prefixes=docs/datadoc/prefixes-process.md
+
+
 # Don't crash pre-commit in case the above fails on GitHub
 exit 0

{tripper-0.4.2 → tripper-0.4.3}/.pre-commit-config.yaml

@@ -19,7 +19,7 @@ ci:
 # hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     - id: end-of-file-fixer
       exclude: ^.*\.(svg)$
@@ -47,14 +47,14 @@ repos:
       args: [--line-length=79]
 
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.8.3
+    rev: 1.8.6
     hooks:
     - id: bandit
       args: ["-r"]
       files: ^tripper/.*$
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.15.0
+    rev: v1.17.1
     hooks:
     - id: mypy
       exclude: ^tests/.*$

{tripper-0.4.2 → tripper-0.4.3}/CHANGELOG.md

@@ -1,6 +1,52 @@
 # Changelog
 
-## [v0.4.2](https://github.com/EMMC-ASBL/tripper/tree/v0.4.2) (2025-04-22)
+## [v0.4.3](https://github.com/EMMC-ASBL/tripper/tree/v0.4.3) (2025-08-19)
+
+[Full Changelog](https://github.com/EMMC-ASBL/tripper/compare/v0.4.2...v0.4.3)
+
+**Closed issues:**
+
+- inconsistent usage when filtering searches [\#396](https://github.com/EMMC-ASBL/tripper/issues/396)
+- correct criterias to criteria [\#392](https://github.com/EMMC-ASBL/tripper/issues/392)
+- Add `hasCurator` and `hasCurationDate` properties to resources [\#390](https://github.com/EMMC-ASBL/tripper/issues/390)
+- Support for documenting not \(yet\) existing resources [\#369](https://github.com/EMMC-ASBL/tripper/issues/369)
+- Make the generated keywords documentation look better [\#365](https://github.com/EMMC-ASBL/tripper/issues/365)
+- Speed up tripper.dataset.save\_data\(\) [\#337](https://github.com/EMMC-ASBL/tripper/issues/337)
+- Example in documentation of  search\_iris iw wrong. [\#323](https://github.com/EMMC-ASBL/tripper/issues/323)
+- get\_jsonld\_context does not support PosixPath [\#322](https://github.com/EMMC-ASBL/tripper/issues/322)
+- Set up a triplestore on the PhysMet Portal [\#315](https://github.com/EMMC-ASBL/tripper/issues/315)
+- Make converting a large table of datasets to RDF faster [\#305](https://github.com/EMMC-ASBL/tripper/issues/305)
+- Ensure dataset is TEM schema compliant [\#293](https://github.com/EMMC-ASBL/tripper/issues/293)
+- Define schema for TEM dataset queries [\#292](https://github.com/EMMC-ASBL/tripper/issues/292)
+
+**Merged pull requests:**
+
+- Updated installation instructions on the readme page. [\#415](https://github.com/EMMC-ASBL/tripper/pull/415) ([jesper-friis](https://github.com/jesper-friis))
+- Add support for Python 3.14 [\#414](https://github.com/EMMC-ASBL/tripper/pull/414) ([jesper-friis](https://github.com/jesper-friis))
+- \[pre-commit.ci\] pre-commit autoupdate [\#412](https://github.com/EMMC-ASBL/tripper/pull/412) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Updated dataset figure [\#410](https://github.com/EMMC-ASBL/tripper/pull/410) ([jesper-friis](https://github.com/jesper-friis))
+- Include sparqlwrapper in dependencies for datadoc [\#409](https://github.com/EMMC-ASBL/tripper/pull/409) ([jesper-friis](https://github.com/jesper-friis))
+- \[pre-commit.ci\] pre-commit autoupdate [\#408](https://github.com/EMMC-ASBL/tripper/pull/408) ([pre-commit-ci[bot]](https://github.com/apps/pre-commit-ci))
+- Updated figures [\#407](https://github.com/EMMC-ASBL/tripper/pull/407) ([jesper-friis](https://github.com/jesper-friis))
+- Date and time literals [\#406](https://github.com/EMMC-ASBL/tripper/pull/406) ([jesper-friis](https://github.com/jesper-friis))
+- Added keywords `hasCurator` and `hasCurationDate` [\#405](https://github.com/EMMC-ASBL/tripper/pull/405) ([jesper-friis](https://github.com/jesper-friis))
+- Build documentation with Python 3.12 [\#404](https://github.com/EMMC-ASBL/tripper/pull/404) ([jesper-friis](https://github.com/jesper-friis))
+- Skip running doctest on session.md if Fuseki is not running [\#403](https://github.com/EMMC-ASBL/tripper/pull/403) ([jesper-friis](https://github.com/jesper-friis))
+- Fix issue \#396 [\#401](https://github.com/EMMC-ASBL/tripper/pull/401) ([jesper-friis](https://github.com/jesper-friis))
+- Updated figure with basic relations [\#400](https://github.com/EMMC-ASBL/tripper/pull/400) ([jesper-friis](https://github.com/jesper-friis))
+- Added \_\_contains\_\_\(\) method to namespace [\#399](https://github.com/EMMC-ASBL/tripper/pull/399) ([jesper-friis](https://github.com/jesper-friis))
+- Run mkdocs with Python 3.13 instead of 3.9 [\#398](https://github.com/EMMC-ASBL/tripper/pull/398) ([jesper-friis](https://github.com/jesper-friis))
+- added a file about how to search and delete resources in the ts [\#397](https://github.com/EMMC-ASBL/tripper/pull/397) ([francescalb](https://github.com/francescalb))
+- Update using criteria in search [\#395](https://github.com/EMMC-ASBL/tripper/pull/395) ([francescalb](https://github.com/francescalb))
+- Keywords inverse [\#394](https://github.com/EMMC-ASBL/tripper/pull/394) ([jesper-friis](https://github.com/jesper-friis))
+- Keywords inverse [\#393](https://github.com/EMMC-ASBL/tripper/pull/393) ([jesper-friis](https://github.com/jesper-friis))
+- Added keywords for documenting characterisation processes [\#391](https://github.com/EMMC-ASBL/tripper/pull/391) ([jesper-friis](https://github.com/jesper-friis))
+- WIP: Update classes [\#388](https://github.com/EMMC-ASBL/tripper/pull/388) ([jesper-friis](https://github.com/jesper-friis))
+- Improved control when storing to the triplestore [\#387](https://github.com/EMMC-ASBL/tripper/pull/387) ([jesper-friis](https://github.com/jesper-friis))
+- Fix test\_markdown\_doctest [\#383](https://github.com/EMMC-ASBL/tripper/pull/383) ([jesper-friis](https://github.com/jesper-friis))
+- Added ureg.get\_quantity\(\) method to units module [\#381](https://github.com/EMMC-ASBL/tripper/pull/381) ([jesper-friis](https://github.com/jesper-friis))
+
+## [v0.4.2](https://github.com/EMMC-ASBL/tripper/tree/v0.4.2) (2025-04-23)
 
 [Full Changelog](https://github.com/EMMC-ASBL/tripper/compare/v0.4.1...v0.4.2)
 

{tripper-0.4.2 → tripper-0.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: tripper
-Version: 0.4.2
+Version: 0.4.3
 Summary: A triplestore wrapper for Python.
 Keywords: triplestore,ontology,RDF
 Author-email: SINTEF <TEAM4.0@sintef.no>
@@ -15,15 +15,22 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
 Classifier: Environment :: Plugins
 Classifier: Natural Language :: English
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
 Requires-Dist: typing-extensions>=4.7.0,<4.13.1; python_version < '3.9'
+Requires-Dist: dlite-python>=0.5.27 ; extra == "backends" and ( python_version<='3.13')
+Requires-Dist: emmontopy>=0.5.0,<0.7.1 ; extra == "backends" and ( python_version<'3.13')
+Requires-Dist: graphviz>=0.20.1,<0.20.2 ; extra == "backends"
+Requires-Dist: numpy<2.1.0 ; extra == "backends" and ( python_version=='3.13')
+Requires-Dist: rdflib>=6.3.0,<7.0.0 ; extra == "backends"
 Requires-Dist: tripper[mappings] ; extra == "datadoc"
-Requires-Dist: PyLD>=2.0.0,<2.0.5 ; extra == "datadoc"
+Requires-Dist: PyLD>=2.0.0,<2.0.5 ; extra == "datadoc" and ( python_version<='3.13')
 Requires-Dist: PyYaml>=3.0.0,<6.0.3 ; extra == "datadoc"
 Requires-Dist: requests>=2.0.0,<3.4.1 ; extra == "datadoc"
+Requires-Dist: sparqlwrapper>=2.0.0,<2.0.1 ; extra == "datadoc"
 Requires-Dist: tripper[pre-commit, docs] ; extra == "dev"
 Requires-Dist: tripper[testing] ; extra == "docs"
 Requires-Dist: mike==2.1.3 ; extra == "docs"
@@ -36,14 +43,8 @@ Requires-Dist: mkdocstrings==0.27.0 ; extra == "docs"
 Requires-Dist: mkdocstrings-python-legacy==0.2.4 ; extra == "docs"
 Requires-Dist: tripper[units] ; extra == "mappings"
 Requires-Dist: pre-commit==4.0.1 ; extra == "pre-commit"
-Requires-Dist: pylint==3.3.4 ; extra == "pre-commit"
-Requires-Dist: tripper[datadoc, mappings, testing-core] ; extra == "testing"
-Requires-Dist: dlite-python>=0.5.27 ; extra == "testing" and ( python_version>='3.8')
-Requires-Dist: emmontopy>=0.5.0,<0.7.1 ; extra == "testing" and ( python_version<'3.13')
-Requires-Dist: graphviz>=0.20.1,<0.20.2 ; extra == "testing"
-Requires-Dist: numpy<2.1.0 ; extra == "testing" and ( python_version>='3.13')
-Requires-Dist: rdflib>=6.3.0,<7.0.0 ; extra == "testing"
-Requires-Dist: sparqlwrapper>=2.0.0,<2.0.1 ; extra == "testing"
+Requires-Dist: pylint==3.3.4 ; extra == "pre-commit" and ( python_version>='3.9')
+Requires-Dist: tripper[datadoc, backends, testing-core] ; extra == "testing"
 Requires-Dist: pytest==8.3.4 ; extra == "testing-core"
 Requires-Dist: pytest-cov==5.0.0 ; extra == "testing-core" and ( python_version<'3.9')
 Requires-Dist: pytest-cov==6.0.0 ; extra == "testing-core" and ( python_version>='3.9')
@@ -56,6 +57,7 @@ Project-URL: Home, https://github.com/EMMC-ASBL/tripper
 Project-URL: Issue Tracker, https://github.com/EMMC-ASBL/tripper/issues
 Project-URL: Package, https://pypi.org/project/tripper
 Project-URL: Source, https://github.com/EMMC-ASBL/tripper
+Provides-Extra: backends
 Provides-Extra: datadoc
 Provides-Extra: dev
 Provides-Extra: docs
@@ -93,10 +95,10 @@ It strives for simplicity and is modelled after [rdflib] (with a few simplificat
 In Tripper:
 
 * All IRIs are represented by Python strings.
-  Example: `"https://w3id.org/emmo#Metre"`
+  Example: `https://w3id.org/emmo#Metre`
 
-* Blank nodes are strings starting with "_:".
-  Example: `"_:bnode1"`
+* Blank nodes are strings starting with `_:`.
+  Example: `_:bnode1`
 
 * Literals are constructed with [`tripper.Literal`][Literal].
   Example: `tripper.Literal(3.14, datatype=XSD.float)`
@@ -137,20 +139,40 @@ Installation
 Tripper has by itself no dependencies outside the standard library, but the triplestore backends may have specific dependencies.
 
 
-The package can be installed from [PyPI] using `pip`:
+The package can be installed from [PyPI] using `pip`.
+A minimal installation can be done with
 
 ```shell
 pip install tripper
 ```
 
-In addition you would need to install the requirements for one or more of the backends listed in the table above.
-For mappings you would also need to install [Pint].
-For example:
+but typically, you would also like to install the requirements needed by the backends, the tripper sub-packages and extra features.
+The requirements for the backends are listed in the table above, while sub-packages and extra features are enabled by specifying one or more of the "extras" listed in the table below when installing Tripper.
+
+
+For example, the following command will install Tripper with the [tripper.datadoc] sub-package and the rdflib backend enabled:
 
 ```shell
-pip install rdflib pint
+pip install tripper[datadoc] rdflib
 ```
 
+Developers should install Tripper with the `dev` extras and enable [pre-commit]:
+
+```shell
+pip install tripper[dev]
+pre-commit install  # Enable pre-commit and installing hooks
+```
+
+
+| Extras   | Description of dependencies                                        | Implies          |
+|----------|--------------------------------------------------------------------|------------------|
+| units    | Required by the [tripper.units] sub-package.                       |                  |
+| mappings | Required by the [tripper.mappings] sub-package.                    | units            |
+| datadoc  | Required by the [tripper.datadoc] sub-package.                     | mappings         |
+| backends | Installs dependencies for all backends                             |                  |
+| testing  | For testing.                                                       | datadoc,backends |
+| docs     | For generation of documentation                                    | testing          |
+| dev      | For developers. Installs all dependencies, including [pre-commit]. | dev              |
 
 
 
@@ -200,4 +222,5 @@ We gratefully acknowledge the following projects for supporting the development
 [StarDog]: https://www.stardog.com/
 [GraphDB]: https://www.ontotext.com/products/graphdb/
 [Pint]: https://pint.readthedocs.io/en/stable/
+[pre-commit]: https://pre-commit.com/
 

{tripper-0.4.2 → tripper-0.4.3}/README.md

@@ -26,10 +26,10 @@ It strives for simplicity and is modelled after [rdflib] (with a few simplificat
 In Tripper:
 
 * All IRIs are represented by Python strings.
-  Example: `"https://w3id.org/emmo#Metre"`
+  Example: `https://w3id.org/emmo#Metre`
 
-* Blank nodes are strings starting with "_:".
-  Example: `"_:bnode1"`
+* Blank nodes are strings starting with `_:`.
+  Example: `_:bnode1`
 
 * Literals are constructed with [`tripper.Literal`][Literal].
   Example: `tripper.Literal(3.14, datatype=XSD.float)`
@@ -70,20 +70,40 @@ Installation
 Tripper has by itself no dependencies outside the standard library, but the triplestore backends may have specific dependencies.
 
 
-The package can be installed from [PyPI] using `pip`:
+The package can be installed from [PyPI] using `pip`.
+A minimal installation can be done with
 
 ```shell
 pip install tripper
 ```
 
-In addition you would need to install the requirements for one or more of the backends listed in the table above.
-For mappings you would also need to install [Pint].
-For example:
+but typically, you would also like to install the requirements needed by the backends, the tripper sub-packages and extra features.
+The requirements for the backends are listed in the table above, while sub-packages and extra features are enabled by specifying one or more of the "extras" listed in the table below when installing Tripper.
+
+
+For example, the following command will install Tripper with the [tripper.datadoc] sub-package and the rdflib backend enabled:
 
 ```shell
-pip install rdflib pint
+pip install tripper[datadoc] rdflib
 ```
 
+Developers should install Tripper with the `dev` extras and enable [pre-commit]:
+
+```shell
+pip install tripper[dev]
+pre-commit install  # Enable pre-commit and installing hooks
+```
+
+
+| Extras   | Description of dependencies                                        | Implies          |
+|----------|--------------------------------------------------------------------|------------------|
+| units    | Required by the [tripper.units] sub-package.                       |                  |
+| mappings | Required by the [tripper.mappings] sub-package.                    | units            |
+| datadoc  | Required by the [tripper.datadoc] sub-package.                     | mappings         |
+| backends | Installs dependencies for all backends                             |                  |
+| testing  | For testing.                                                       | datadoc,backends |
+| docs     | For generation of documentation                                    | testing          |
+| dev      | For developers. Installs all dependencies, including [pre-commit]. | dev              |
 
 
 
@@ -133,3 +153,4 @@ We gratefully acknowledge the following projects for supporting the development
 [StarDog]: https://www.stardog.com/
 [GraphDB]: https://www.ontotext.com/products/graphdb/
 [Pint]: https://pint.readthedocs.io/en/stable/
+[pre-commit]: https://pre-commit.com/

tripper-0.4.3/docs/datadoc/classdoc.md

@@ -0,0 +1,60 @@
+Documenting abstract resources
+------------------------------
+Resources that do not exist are called *abstract resources*.
+A typical example of an abstract resource is a procedure that has not been performed (yet), like a general description of a task in a workflow.
+
+It is highly desirable to document such a resource as a class (i.e. in the TBox).
+It is consistent with the physicalistic/nominalistic approach taken by major ontological frameworks for applied sciences and makes it easy to document actual executions of such a workflow task as an individual of this class.
+
+```python
+{
+    "@id": "ex:MySimulation",
+    "@type": "owl:Class",
+    "subClassOf": "PhysicsBasedSimulation",
+    "prefLabel": "MySimulation",
+    "elucidation": "A simulation using my physics-based materials models.",
+    "isParticipatedBy": {
+        "@id": "ex:MyModel",
+        "@type": "owl:Class"  # restrictionType defaults to some
+    },
+    "command": "mymodel infile.txt -o outfile.txt",  # Command to execute the model
+    "workdir": ".",  # Relative path to working directory
+    "environment": {"VAR1": "val1", "VAR2": "val2"},  # Environment variables (JSON-encoded)
+    "install_command": "pip install git+ssh://git@github.com:MyProj/myrepo.git@master",
+    "hasInput": [
+        {
+            "@id": "ex:MyInputDataset",
+            "@type": "owl:Class",
+            "subClassOf": ["dcat:Dataset", "emmo:Dataset"],
+            "restrictionType": "exactly 1",  # defaults to "some"
+            "prefLabel": "MyInputDataset.",
+            "elucidation": "My input dataset.",
+            "distribution": {
+                "accessURL": "file:./infile.txt",
+                "accessService": {
+                    "conformsTo": "https://github.com/SINTEF/dlite/",
+                    "generator": "ex:inputplugin"  # for generating input
+                }
+            }
+        }
+    ],
+    "hasOutput": [
+        {
+            "@id": "ex:MyOutputDataset",
+            "@type": "owl:Class",
+            "subClassOf": ["dcat:Dataset", "emmo:Dataset"],
+            "restrictionType": "exactly 1",  # defaults to "some"
+            "prefLabel": "MyOutputDataset.",
+            "elucidation": "My output dataset.",
+            "distribution": {
+                "accessURL": "file:./outfile.txt",
+                "accessService": {
+                    "conformsTo": "https://github.com/SINTEF/dlite/",
+                    "parser": "ex:outputplugin",  # for parsing output
+                    "generator": "ex:outputplugin"  # for storing output to external storage
+                }
+            }
+        }
+    ]
+}
+```

{tripper-0.4.2 → tripper-0.4.3}/docs/datadoc/customisation.md

@@ -13,7 +13,7 @@ Tripper already include a default list of [predefined prefixes].
 Additional prefixed can be provided in two ways.
 
 ### With the `prefixes` argument
-Several functions in the API (like [save_dict()], [told()] and [TableDoc.parse_csv()]) takes a `prefixes` argument with which additional namespace prefixes can provided.
+Several functions in the API (like [store()], [told()] and [TableDoc.parse_csv()]) takes a `prefixes` argument with which additional namespace prefixes can provided.
 
 This may be handy when used from the Python API.
 
@@ -177,9 +177,9 @@ You can save this context to a triplestore with
 >>> ts = Triplestore("rdflib")
 >>> save_datadoc(  # doctest: +ELLIPSIS
 ...     ts,
-...      "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/custom_context.yaml",
+...     "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/custom_context.yaml",
 ... )
-AttrDict(...)
+{'@context': ...}
 
 ```
 
@@ -191,25 +191,31 @@ The content of the triplestore should now be
 @prefix dcat: <http://www.w3.org/ns/dcat#> .
 @prefix kb: <http://example.com/kb#> .
 @prefix myonto: <http://example.com/myonto#> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 <BLANKLINE>
-kb:sampleA a dcat:Resource,
+kb:sampleA a rdfs:Resource,
+        dcat:Resource,
         chameo:Sample ;
     myonto:fromBatch kb:batch1 .
 <BLANKLINE>
-kb:sampleB a dcat:Resource,
+kb:sampleB a rdfs:Resource,
+        dcat:Resource,
         chameo:Sample ;
     myonto:fromBatch kb:batch1 .
 <BLANKLINE>
-kb:sampleC a dcat:Resource,
+kb:sampleC a rdfs:Resource,
+        dcat:Resource,
         chameo:Sample ;
     myonto:fromBatch kb:batch2 .
 <BLANKLINE>
 kb:batch2 a myonto:Batch,
+        rdfs:Resource,
         dcat:Resource ;
     myonto:batchNumber 2 .
 <BLANKLINE>
 kb:batch1 a myonto:Batch,
+        rdfs:Resource,
         dcat:Resource ;
     myonto:batchNumber 1 .
 <BLANKLINE>
@@ -239,10 +245,11 @@ Instead, the list of available resource types should be stored and retrieved fro
 [Python dict]: #python-dict
 [resource types]: introduction.md#resource-types
 [Documenting a resource]: documenting-a-resource.md
+[Search for and fetching resources]: fetching-resources-from-a-triplestore.md
 [predefined prefixes]: prefixes.md
 [predefined keywords]: keywords.md
 [default context]: https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.2/context.json
-[save_dict()]: ../api_reference/datadoc/dataset.md#tripper.datadoc.dataset.save_dict
+[store()]: ../api_reference/datadoc/dataset.md#tripper.datadoc.dataset.store
 [told()]: ../api_reference/datadoc/dataset.md#tripper.datadoc.dataset.told
 [save_datadoc()]: ../api_reference/datadoc/dataset.md#tripper.datadoc.dataset.save_datadoc
 [TableDoc]: ../api_reference/datadoc/tabledoc.md/#tripper.datadoc.tabledoc.TableDoc

{tripper-0.4.2 → tripper-0.4.3}/docs/datadoc/documenting-a-resource.md

@@ -1,7 +1,7 @@
 Documenting a resource
 ======================
-In the [tripper.datadoc] sub-package are the documents documenting the resources internally represented as [JSON-LD] documents stored as Python dicts.
-However, the API tries to hide away the complexities of JSON-LD behind simple interfaces.
+In the [tripper.datadoc] sub-package, the documents documenting the resources internally represented as [JSON-LD] documents are stored as Python dicts.
+However, the API tries to hide the complexities of JSON-LD behind simple interfaces.
 To support different use cases, the sub-package provide several interfaces for data documentation, including Python dicts, YAML files and tables.
 These are further described below.
 
@@ -37,7 +37,7 @@ We therefore have to define them explicitly
 
 ```python
 >>> prefixes = {
-...     "sem": "https://w3id.com/emmo/domain/sem/0.1#",
+...     "sem": "https://w3id.org/emmo/domain/sem/0.1#",
 ...     "kb": "http://example.com/kb/"
 ... }
 
@@ -60,7 +60,7 @@ We therefore have to define them explicitly
     {
         "@context": "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tripper/context/0.3/context.json",
         "@id": "http://example.com/kb/image1",
-        "@type": "https://w3id.com/emmo/domain/sem/0.1#SEMImage",
+        "@type": "https://w3id.org/emmo/domain/sem/0.1#SEMImage",
         "creator": {
             "@type": [
                 "http://xmlns.com/foaf/0.1/Agent",
@@ -77,14 +77,14 @@ We therefore have to define them explicitly
     }
     ```
 
-You can use [save_dict()] to save this documentation to a triplestore.
+You can use [store()] to save this documentation to a triplestore.
 Since the prefixes "sem" and "kb" are not included in the [Predefined prefixes], they are have to be provided explicitly.
 
 ```python
 >>> from tripper import Triplestore
->>> from tripper.datadoc import save_dict
+>>> from tripper.datadoc import store
 >>> ts = Triplestore(backend="rdflib")
->>> d = save_dict(ts, dataset, prefixes=prefixes)
+>>> d = store(ts, dataset, prefixes=prefixes)
 
 ```
 
@@ -104,7 +104,7 @@ You can use `ts.serialize()` to list the content of the triplestore (defaults to
 @prefix foaf: <http://xmlns.com/foaf/0.1/> .
 @prefix kb: <http://example.com/kb/> .
 @prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
-@prefix sem: <https://w3id.com/emmo/domain/sem/0.1#> .
+@prefix sem: <https://w3id.org/emmo/domain/sem/0.1#> .
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 
 kb:image1 a sem:SEMImage ;
@@ -119,7 +119,7 @@ kb:image1 a sem:SEMImage ;
 ```
 
 Note that the image implicitly has been declared to be an individual of the classes `dcat:Dataset` and `emmo:Dataset`.
-This is because the `type` argument of [save_dict()] defaults to "dataset".
+This is because the `type` argument of [store()] defaults to "dataset".
 
 
 ### Multi-resource dict
@@ -145,11 +145,11 @@ Saving [semdata.yaml] to a triplestore can e.g. be done with
 
 ```python
 >>> from tripper.datadoc import save_datadoc
->>> save_datadoc(  # doctest: +ELLIPSIS
+>>> save_datadoc(  # doctest: +ELLIPSIS, +NORMALIZE_WHITESPACE
 ...    ts,
 ...    "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.yaml"
 ... )
-AttrDict(...)
+{'@graph': [...], ...}
 
 ```
 
@@ -186,7 +186,7 @@ The below example shows how to save all datasets listed in the CSV file [semdata
 >>> td = TableDoc.parse_csv(
 ...     "https://raw.githubusercontent.com/EMMC-ASBL/tripper/refs/heads/master/tests/input/semdata.csv",
 ...     prefixes={
-...         "sem": "https://w3id.com/emmo/domain/sem/0.1#",
+...         "sem": "https://w3id.org/emmo/domain/sem/0.1#",
 ...         "semdata": "https://he-matchmaker.eu/data/sem/",
 ...         "sample": "https://he-matchmaker.eu/sample/",
 ...         "mat": "https://he-matchmaker.eu/material/",
@@ -215,7 +215,7 @@ The below example shows how to save all datasets listed in the CSV file [semdata
 [emmo:Dataset]: https://w3id.org/emmo#EMMO_194e367c_9783_4bf5_96d0_9ad597d48d9a
 [oteio:Generator]: https://w3id.org/emmo/domain/oteio/Generator
 [oteio:Parser]: https://w3id.org/emmo/domain/oteio/Parser
-[save_dict()]: ../api_reference/datadoc/dataset.md/#tripper.datadoc.dataset.save_dict
+[store()]: ../api_reference/datadoc/dataset.md/#tripper.datadoc.dataset.store
 [told()]: ../api_reference/datadoc/dataset.md/#tripper.datadoc.dataset.told
 [save_datadoc()]:
 ../api_reference/datadoc/dataset.md/#tripper.datadoc.dataset.save_datadoc